Examples of Coordinate Definitions: Formic acid

A MOPAC data set normally consists of one line of keywords, two lines of user-defined text, then the Z-matrix.  In this example, normal internal coordinates are used for all atoms.   After the Z-matrix there should be either a blank line or a line of zero's (as shown here).

AM1
Formic acid
Example of normal geometry definition
   O    0.0  0    0.0 0    0.0 0   0  0  0
   C    1.20 1    0.0 0    0.0 0   0  0  0
   O    1.32 1  116.8 1    0.0 0   2  1  0
   H    0.98 1  123.9 1    0.0 0   3  2  1
   H    1.11 1  127.3 1  180.0 0   2  1  3
   0    0.00 0    0.0 0    0.0 0   0  0  0

includegraphics{pichcooh}
 

The geometry in this data-set can be understood as follows: Atom 1, an oxygen, is at the origin of internal coordinate space, and has coordinates (0,0,0). Atom 2, a carbon, is positioned at coordinate (1.20,0,0), that is, it is related to the oxygen by a bond-length of 1.20 Ångstroms, and to atom 3, an oxygen, by a bond-length of 1.32 Ångstroms. The O-C-O angle is 116.8 degrees. The first hydrogen is bonded to the hydroxyl oxygen and the second hydrogen is bonded to the carbon atom. The H-C-O-O dihedral angle is 180 degrees.